An accessible, efficient and global approach for the large-scale sequencing of bacterial genomes
| Autor: | Jay C. D. Hinton, Ross Low, Blanca M. Perez-Sepulveda, J Lipscombe, Kate S. Baker, Nicholas A. Feasey, Hermione J. Webster, Will P. M. Rowe, Darren Heavens, Chris Watkins, Benjamin Kumwenda, Christian Schudoma, Karl Costigan, Caisey V. Pulford, Neil Hall, Alexander V. Predeus, Neil Shearer |
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| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
DNA
Bacterial Thermolysates QH301-705.5 Method Computational biology Bacterial genome size Biology QH426-470 Genome DNA sequencing iNTS 03 medical and health sciences 0302 clinical medicine Salmonella Genetics Humans Biology (General) Illumina dye sequencing Ecology Evolution Behavior and Systematics 030304 developmental biology 0303 health sciences Whole-genome sequencing Whole Genome Sequencing 030306 microbiology Salmonella enterica Cell Biology DNA extraction Pipeline (software) Large-Scale Sequencing Genome Bacterial 030217 neurology & neurosurgery |
| Zdroj: | Genome Biology, Vol 22, Iss 1, Pp 1-18 (2021) GENOME BIOLOGY The 10KSG consortium 2021, ' An accessible, efficient and global approach for the large-scale sequencing of bacterial genomes ', Genome Biology, vol. 22, no. 1, 349 . https://doi.org/10.1186/s13059-021-02536-3 Genome Biology |
| ISSN: | 1474-7596 |
| Popis: | We have developed an efficient and inexpensive pipeline for streamlining large-scale collection and genome sequencing of bacterial isolates. Evaluation of this method involved a worldwide research collaboration focused on the model organism Salmonella enterica, the 10KSG consortium. By optimising a logistics pipeline that collected isolates as thermolysates, permitting shipment in ambient conditions, the project assembled a diverse collection of 10,419 clinical and environmental isolates from low- and middle-income countries in less than one year. The bacteria were obtained from 51 countries/territories dating from 1949 to 2017, with a focus on Africa and Latin-America. All isolates were collected in barcoded tubes and genome sequenced using an optimised DNA extraction method and the LITE pipeline for library construction. After Illumina sequencing, the total reagent cost was less than USD$10 per genome. Our method can be applied to genome-sequence other large bacterial collections at a relatively low cost, within a limited timeframe, to support global collaborations. |
| Databáze: | OpenAIRE |
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